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September Update: OpenPandemics - COVID-19

World Community Grid - Št, 17.09.2020 - 18:15
The researchers and the World Community Grid tech team are continuing their work to get the project working on GPU.
Kategórie: Novinky z projektov

September Update: Help Stop TB

World Community Grid - St, 16.09.2020 - 18:44
The Help Stop TB researchers will soon have an additional team member to help with data analysis for a couple of months.
Kategórie: Novinky z projektov

Open-source software program helps power 30 years of progress in computational research

World Community Grid - Po, 14.09.2020 - 18:42
AutoDock, the software program that powers OpenPandemics and other World Community Grid projects, was created 30 years ago at Scripps Research. Learn more about this powerful software in this article and the attached, recently-published research paper.
Kategórie: Novinky z projektov

September Update: FightAIDS@Home

World Community Grid - Pi, 11.09.2020 - 18:52
The researchers are in the early stages of exploring new possibilities for the next phase of the project.
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Tenth anniversary of the first Einstein@Home discovery

Einstein@Home - Št, 10.09.2020 - 07:39

Ten years ago, Einstein@Home published its first astronomical discovery. The radio pulsar J2007+2722 was found in July 2010 with our radio pulsar search, analyzing data from the Arecibo Radio Telescope. The discovery appeared in print on 10 September 2010. A more detailed article about the discovery was published later.

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Kategórie: Novinky z projektov

September Update: Africa Rainfall Project

World Community Grid - St, 09.09.2020 - 20:18
The Africa Rainfall Project researchers recently welcomed a student to their team.
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New paper: Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations.

GPUGRID - St, 09.09.2020 - 11:24
Another great GPUGRID-based work: studying the possible modulation of intrinsically disordered proteins through drugs. Herrera-Nieto P, Pérez A, De Fabritiis G, Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of chemical information and modeling 2020. doi:10.1021/acs.jcim.0c00381 The corresponding badge is labeled "Herrera-Nieto, JCIM 2020". The extreme dynamic behavior of intrinsically disordered proteins hinders the development of drug-like compounds capable of modulating them. There are several examples of small molecules that specifically interact with disordered peptides. However, their mechanisms of action are still not well understood. Here, we use extensive molecular dynamics simulations combined with adaptive sampling algorithms to perform free ligand binding studies in the context of intrinsically disordered proteins. We tested this approach in the system composed by the D2 sub-domain of the disordered protein p27 and the small molecule SJ403. The results show several protein–ligand bound states characterized by the establishment of a loosely oriented interaction mediated by a limited number of contacts between the ligand and critical residues of p27. Finally, protein conformations in the bound state are likely to be explored by the isolated protein too, therefore supporting a model where the addition of the small molecule restricts the available conformational space.
Kategórie: Novinky z projektov

Thanks for supporting SixTrack at LHC@Home and updates

LHC@home - Ut, 23.01.2018 - 19:08
Dear volunteers,

All members of the SixTrack team would like to thank each of you for supporting our project at LHC@Home. The last weeks saw a significant increase in work load, and your constant help did not pause even during the Christmas holidays, which is something that we really appreciate!

As you know, we are interested in simulating the dynamics of the beam in ultra-relativistic storage rings, like the LHC. As in other fields of physics, the dynamics is complex, and it can be decomposed into a linear and a non-linear part. The former allows the expected performance of the machine to be at reach, whereas the latter might dramatically affect the stability of the circulating beam. While the former can be analysed with the computing power of a laptop, the latter requires BOINC, and hence you! In fact, we perform very large scans of parameter spaces to see how non-linearities affect the motion of beam particles in different regions of the beam phase space and for different values of key machine parameters. Our main observable is the dynamic aperture (DA), i.e. the boundary between stable, i.e. bounded, and unstable, i.e., unbounded, motion of particles.

The studies mainly target the LHC and its upgrade in luminosity, the so-called HL-LHC. Thanks to this new accelerator, by ~2035, the LHC will be able to deliver to experiments x10 more data than what is foreseen in the first 10/15y of operation of LHC in a comparable time. We are in full swing in designing the upgraded machine, and the present operation of the LHC is a unique occasion to benchmark our models and simulation results. The deep knowledge of the DA of the LHC is essential to properly tune the working point of the HL-LHC.

If you have crunched simulations named "workspace1_hl13_collision_scan_*" (Frederik), then you have helped us in mapping the effects of unavoidable magnetic errors expected from the new hardware of the HL-LHC on dynamic aperture, and identify the best working point of the machine and correction strategies. Tasks named like "w2_hllhc10_sqz700_Qinj_chr20_w2*" (Yuri) focus the attention onto the magnets responsible for squeezing the beams before colliding them; due to their prominent role, these magnets, very few in number, have such a big impact on the non-linear dynamics that the knobs controlling the linear part of the machine can offer relevant remedial strategies.

Many recent tasks are aimed at relating the beam lifetime to the dynamic aperture. The beam lifetime is a measured quantity that tells us how long the beams are going to stay in the machine, based on the current rate of losses. A theoretical model relating beam lifetime and dynamic aperture was developed; a large simulation campaign has started, to benchmark the model against plenty of measurements taken with the LHC in the past three years. One set of studies, named "w16_ats2017_b2_qp_0_ats2017_b2_QP_0_IOCT_0" (Pascal), considers as main source of non-linearities the unavoidable multipolar errors of the magnets, whereas tasks named as "LHC_2015*" (Javier) take into account the parasitic encounters nearby the collision points, i.e. the so called "long-range beam-beam effects".

One of our users (Ewen) is carrying out two studies thanks to your help. In 2017 DA was directly measured for the first time in the LHC at top energy, and nonlinear magnets on either side of ATLAS and CMS experiments were used to vary the DA. He wants to see how well the simulated DA compares to these measurements. The second study seeks to look systematically at how the time dependence of DA in simulation depends on the strength of linear transverse coupling, and the way it is generated in the machine. In fact, some previous simulations and measurements at injection energy have indicated that linear coupling between the horizontal and vertical planes can have a large impact on how the dynamic aperture evolves over time.

In all this, your help is fundamental, since you let us carry out the simulations and studies we are interested in, running the tasks we submit to BOINC. Hence, the warmest "thank you" to you all!
Happy crunching to everyone, and stay tuned!

Alessio and Massimo, for the LHC SixTrack team.
Kategórie: Novinky z projektov

LHC@home down-time due to system updates

LHC@home - Ut, 23.01.2018 - 11:19
Tomorrow Wednesday 24/1, the LHC@home servers will be unavailable for a short period while our storage backend is taken down for a system update.

Today, Tuesday 23/1, some of the Condor servers that handle CMS, LHCb and Theory tasks will be down for a while. Regarding the on-going issues with upload of files, please refer to this thread.

Thanks for your understanding and happy crunching!
Kategórie: Novinky z projektov
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